The scripts are used to analyze single cell RNA sequencing data in the paper "Tumor Microenvironment Remodeling after Neoadjuvant Immunotherapy in Non-small Cell Lung Cancer Revealed by Single-Cell RNA Sequencing", including quality control, clustering, CopyKat, trajectory, CellPhoneDB, Nichenet, and SCENIC analyses. The scripts need modification accroding to the comments(##) in the script before running.